Biomedical subjects

Carmelo Giacovazzo

Publications and source records attributed to Carmelo Giacovazzo.

8 recordsLinked to original sources

PubMed2003

Ab initio protein phasing at 1.4 A resolution.

All the techniques today available for the ab initio crystal structure solution of proteins require that the atomicity condition is satisfied. Accordingly, diffraction data at resolution equal or better than 1.2 A are necessary. This condition reduces the role of the ab initio techniques in macromolecular crystallography. The computer program SIR2002 has been modified in such a way that it may succeed also with 1.4 A resolution diffraction data. The modifications concern all the modules of the program: the modified program also benefits by the efficiency of a figure of merit.

Collagen↗

PubMed2003

The estimate of the protein phases for the SAD case: a simplified formula.

The probabilistic formula derived via the rigorous method of the joint probability distribution function to estimate protein phases in the single-wavelength anomalous diffraction (SAD) case [Giacovazzo & Siliqi (2001). Acta Cryst. A57, 40-46] has been revised. A simple but equally effective formula is provided, allowing an easy interpretation of the role of the structural parameters accessible via a diffraction experiment. In particular, the formula is able to simultaneously combine the contribution arising from the anomalous differences with a Sim-like contribution, and also to take the errors into account.

Models, Molecular↗

PubMed2003

SAD or MAD phasing: location of the anomalous scatterers.

The method of joint probability distribution functions is applied in order to estimate the structure-factor moduli of the anomalous scatterer substructure both in the SAD (single-wavelength anomalous dispersion) and in the MAD (multi-wavelength anomalous dispersion) cases. The experimental data |F(1)(+)|, |F(1)(-)|, ..., |F(n)(+)|, |F(n)(-)| measured at n wavelengths are used simultaneously to estimate the value of |F(oa)| arising from the normal scattering of the anomalous scatterers. A practical procedure is described that, when applied to the experimental diffraction data of several proteins, shows robustness and efficiency.

Algorithms↗

PubMed2002

The method of joint probability distribution functions applied to SIR-MIR and to SIRAS-MIRAS cases.

SIR-MIR and SIRAS-MIRAS cases are studied by application of the joint probability distribution method. The final results are conditional probability distributions of the protein phases given the structure-factor moduli of the protein and of the derivatives, and the structure factors of the heavy-atom substructures. The approach is able to treat errors arising from measurements, from the heavy-atom structure model and from the lack of isomorphism. The relations between the present approach and previous methods are described. The formulas have been implemented in a procedure that is able to automatically phase protein reflections up to protein resolution [Giacovazzo, Ladisa & Siliqi (2002). Acta Cryst. A58, 598-604].

Algorithms↗

PubMed2002

Crystal structure solution of proteins by direct methods: an automatic procedure for SIR-MIR and SIRAS-MIRAS cases.

In the previous paper [Giacovazzo & Siliqi (2002). Acta Cryst. A58, 590-597], a probabilistic approach for the SIR-MIR and the SIRAS-MIRAS cases has been described. The mathematical technique is able to take into account the errors arising from measurements, lack of isomorphism and heavy-atom model substructure. An automatic procedure is here described in which the conclusive formulas of that probabilistic approach have been implemented. The procedure has been successfully applied to several test structures: it can automatically provide, starting from the experimental data, high-quality electron-density maps.

Journal Article↗

PubMed2002

Confined structures: basic crystallographic aspects.

The concept of a confined structure is introduced. The statistical properties of the structure factors for such structures are derived and the main features of the Patterson function are described. It is shown that the structure-factor distributions for the confined structures coincide with those derived for the rational index reflections of ordinary structures. Algorithms potentially useful for protein crystal structure solution are identified and checked via experimental applications.

Journal Article↗

PubMed2002

MAD phasing: probabilistic estimate of [F (oa)].

The method of the joint probability distribution function is applied in order to estimate the structure-factor moduli of the anomalous scatterer substructure. The two-wavelength case is examined: the prior knowledge of the moduli [F(1)(+)], [F(1)(-)], [F(2)(+)], [F(2)(-)] is used to predict the value of [F(oa)] arising from the normal scattering of the anomalous scatterers. The conclusive formula is applied to ideal and to real cases: evidence of the usefulness of the approach is obtained.

Computational Biology↗

PubMed2002

Direct methods and isomorphous replacement. The triplet invariant estimate when heavy atoms are located.

The probabilistic theory of the three-phase structure invariants for isomorphous pairs has been generalized to the case in which a heavy-atom structure model is available. The rigorous method of joint probability distributions has been applied: it is able to handle errors in measurements and in the heavy-atom structure model, as well as the lack of isomorphism. The conclusive formulas have been successfully applied to experimental data.

Journal Article↗